Olivier Lichtarge

According to our database, Olivier Lichtarge authored at least 32 papers between 1986 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in <i>E.coli</i> and <i>B.subtilis</i>.

Chen Wang, Harikumar Govindarajan, Panagiotis Katsonis, Olivier Lichtarge

Bioinform., August, 2023

2021

Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family.

Chen Wang, Daniel M. Konecki, David C. Marciano, Harikumar Govindarajan, Amanda M. Williams, Brigitta Wastuwidyaningtyas, Thomas Bourquard, Panagiotis Katsonis, Olivier Lichtarge

Bioinform., November, 2021

Using interpretable deep learning to model cancer dependencies.

Chih-Hsu Lin, Olivier Lichtarge

Bioinform., 2021

2020

An Evolutionary Trace method defines functionally important bases and sites common to RNA families.

Ilya B. Novikov, Angela D. Wilkins, Olivier Lichtarge

PLoS Comput. Biol., 2020

Discovery of disease- and drug-specific pathways through community structures of a literature network.

Minh Pham, Stephen J. Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge

Bioinform., 2020

Graph-Based Information Diffusion Method for Prioritizing Functionally Related Genes in Protein-Protein Interaction Networks.

Minh Pham, Olivier Lichtarge

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

2019

Multimodal network diffusion predicts future disease-gene-chemical associations.

Chih-Hsu Lin, Daniel M. Konecki, Meng Liu, Stephen J. Wilson, Huda Nassar, Angela D. Wilkins, David F. Gleich, Olivier Lichtarge

Bioinform., 2019

2017

Discovery of Functional and Disease Pathways by Community Detection in Protein-Protein Interaction Networks.

Stephen J. Wilson, Angela D. Wilkins, Chih-Hsu Lin, Rhonald C. Lua, Olivier Lichtarge

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Human Kinases Display Mutational Hotspots at Cognate Positions Within Cancer.

Jonathan Gallion, Angela D. Wilkins, Olivier Lichtarge

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

2016

UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

Rhonald C. Lua, Stephen J. Wilson, Daniel M. Konecki, Angela D. Wilkins, Eric Venner, Daniel H. Morgan, Olivier Lichtarge

Nucleic Acids Res., 2016

Computing Therapy for Precision Medicine: Collaborative Filtering Integrates and Predicts Multi-entity Interactions.

Sam Regenbogen, Angela D. Wilkins, Olivier Lichtarge

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Repurposing Germline Exomes of the Cancer Genome Atlas Demands a Cautious Approach and Sample-Specific Variant Filtering.

Amanda Koire, Panagiotis Katsonis, Olivier Lichtarge

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2015

Predicting Future Scientific Discoveries Based on a Networked Analysis of the Past Literature.

Meenakshi Nagarajan, Angela D. Wilkins, Benjamin J. Bachman, Ilya B. Novikov, Shenghua Bao, Peter J. Haas, María E. Terrón-Díaz, Sumit Bhatia, Anbu K. Adikesavan, Jacques J. Labrie, Sam Regenbogen, Christie M. Buchovecky, Curtis R. Pickering, Linda Kato, Andreas Martin Lisewski, Ana Lelescu, Houyin Zhang, Stephen Boyer, Griff Weber, Ying Chen, Lawrence A. Donehower, W. Scott Spangler, Olivier Lichtarge

Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2015

2014

Automated hypothesis generation based on mining scientific literature.

W. Scott Spangler, Angela D. Wilkins, Benjamin J. Bachman, Meena Nagarajan, Tajhal Dayaram, Peter J. Haas, Sam Regenbogen, Curtis R. Pickering, Austin Comer, Jeffrey N. Myers, Ioana Stanoi, Linda Kato, Ana Lelescu, Jacques J. Labrie, Neha Parikh, Andreas Martin Lisewski, Lawrence A. Donehower, Ying Chen, Olivier Lichtarge

Proceedings of the 20th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2014

2013

Function prediction from networks of local evolutionary similarity in protein structure.

Serkan Erdin, Eric Venner, Andreas Martin Lisewski, Olivier Lichtarge

BMC Bioinform., 2013

Accounting for epistatic interactions improves the functional analysis of protein structures.

Angela D. Wilkins, Eric Venner, David C. Marciano, Serkan Erdin, Benu Atri, Rhonald C. Lua, Olivier Lichtarge

Bioinform., 2013

2012

ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape.

Benjamin J. Bachman, Eric Venner, Rhonald C. Lua, Serkan Erdin, Olivier Lichtarge

Bioinform., 2012

2010

PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes.

Rhonald C. Lua, Olivier Lichtarge

Bioinform., 2010

2009

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates.

R. Matthew Ward, Eric Venner, Bryce Daines, Stephen Murray, Serkan Erdin, David M. Kristensen, Olivier Lichtarge

Bioinform., 2009

2008

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

David M. Kristensen, R. Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y. Chen, Viacheslav Fofanov, Marek Kimmel, Lydia E. Kavraki, Olivier Lichtarge

BMC Bioinform., 2008

2007

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs.

Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki

J. Comput. Biol., 2007

Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction.

Brian Y. Chen, Drew H. Bryant, Viacheslav Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki

J. Bioinform. Comput. Biol., 2007

Background frequencies for residue variability estimates: BLOSUM revisited.

I. Mihalek, I. Res, Olivier Lichtarge

BMC Bioinform., 2007

Graph sharpening plus graph integration: a synergy that improves protein functional classification.

Hyunjung Shin, Andreas Martin Lisewski, Olivier Lichtarge

Bioinform., 2007

Graph-Based Protein Functional Classification.

Hyunjung Shin, Andreas Martin Lisewski, Olivier Lichtarge

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007

2006

ET viewer: an application for predicting and visualizing functional sites in protein structures.

Daniel H. Morgan, David M. Kristensen, David Mittelman, Olivier Lichtarge

Bioinform., 2006

Evolutionary trace report_maker: a new type of service for comparative analysis of proteins.

I. Mihalek, I. Res, Olivier Lichtarge

Bioinform., 2006

A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins.

I. Mihalek, I. Res, Olivier Lichtarge

Bioinform., 2006

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction.

Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki

Proceedings of the Research in Computational Molecular Biology, 2006

2005

An evolution based classifier for prediction of protein interfaces without using protein structures.

I. Res, I. Mihalek, Olivier Lichtarge

Bioinform., 2005

Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs.

Brian Y. Chen, Viacheslav Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki

Proceedings of the Biocomputing 2005, 2005

1986

PROTEAN: Deriving Protein Structure from Constraints.

Barbara Hayes-Roth, Bruce G. Buchanan, Olivier Lichtarge, Mike Hewitt, Russ B. Altman, James F. Brinkley, Craig Cornelius, Bruce S. Duncan, Oleg Jardetzky

Proceedings of the 5th National Conference on Artificial Intelligence. Philadelphia, 1986